User: Rory Stark

gravatar for Rory Stark
Rory Stark2.5k
Reputation:
2,490
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Trusted
Location:
CRUK, Cambridge, UK
Last seen:
1 week, 3 days ago
Joined:
5 years, 6 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 442 results • page 1 of 45 • next >
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Comment: C: DiffBind MA plot
... I'll put it on the list! ...
written 10 days ago by Rory Stark2.5k
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Comment: C: DESeq2 baseMean from DiffBind summarizedExperiment
... In this case, where the count score is DBA_SCORE_READS, the binding matrix does not have pileup scores, but rather the total number of reads that align overlapping each (consensus) peak. This is similar to what you get in RNA data, where the expression matrix has the raw number of reads that overlap ...
written 10 days ago by Rory Stark2.5k
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Comment: C: DiffBind differential binding normalization with different levels of binding
... If you want to use DESeq2, you can set the scaling factor directly using the number of reads in each library: > libsize = as.integer(myDBA$class[8,]) and then set these instead of calling estimateSizeFactors(): > DESeq2::sizeFactors(myDESeq2) <- libsize/min(libsize) ...
written 10 days ago by Rory Stark2.5k
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Comment: C: DiffBind: dba.overlap error
... Yep, you got it. The DBA object that results after the consensus peakset is formed (by calling dba.count()) loses information about peaks that are not in the consensus. As the default is to include all peaks in at least two peaksets, the number of peaks that are in at least one sample and those that ...
written 11 days ago by Rory Stark2.5k
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Answer: A: Question of DiffBind for ChIP-Seq analysis
... As you are now specifying a contrast when calling the plot() function (really dba.plotHeatmap()), it is always plotting using the global binding matrix. In order to get plots based on the differentially bound sites, you need to add contrast=n to the call, where n is the number of the comparison. You ...
written 11 days ago by Rory Stark2.5k
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Answer: A: How to get the list of genes from DiffBind dba.report or dba.peakset
... There are a number of annotation packages available that can work on the GRanges object returned by dba.report() or a bed file. Within Bioconductor, ChIPpeakAnno is popular -- many DiffBind users feed the results into ChIPpeakAnno. ...
written 16 days ago by Rory Stark2.5k
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Answer: A: Differential ChIP-seq analysis
... Input reads can also be used to identify to problematic regions to be filtered from further analysis, ie blacklisting. You should already be using the derived blacklists as per the ENCODE guidelines to filter reads. You can also use the GreyListChIP package to identify anomalous enrichment in your I ...
written 6 weeks ago by Rory Stark2.5k
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Comment: C: Changing box plot font sizes for axes and labels in DiffBind
... Bug has been logged and will be fixed. -R ...
written 9 weeks ago by Rory Stark2.5k
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Answer: A: getting DiffBind full result list
... You can get stats for all the peaks by setting th=1 in the call to dba.report(). It's worth noting that it is not necessarily the case that peaks with higher FDR values are not changing, rather that there is insufficient evidence to be confident that they did change (potentially due to e.g. inadequ ...
written 10 weeks ago by Rory Stark2.5k
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Answer: A: change x- and y-axis limit within dba.plotVolcano in DiffBind
... dba.plotVocano() uses ggplot internally, so ylim() doesn'y work. There is no easy way to change the behavior of dba.plotVolcano(). If you assign the return value of the call to dba.plotVolcano(), you will get a GRanges object with all the data you need to make your own plots. For example: > da ...
written 10 weeks ago by Rory Stark2.5k

Latest awards to Rory Stark

Scholar 12 weeks ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 14 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 14 months ago, created an answer that has been accepted. For A: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
Scholar 14 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 14 months ago, created a question with more than 1,000 views. For diffbind
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 14 months ago, created an answer that has been accepted. For A: Diffbind: dba.plot retrieve variance explained
Scholar 14 months ago, created an answer that has been accepted. For A: DiffBind - Losing replicate information?
Scholar 14 months ago, created an answer that has been accepted. For A: DiffBind dba.analyze() to return all differentially enriched peaks?
Popular Question 14 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 14 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Scholar 14 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 14 months ago, created an answer that has been accepted. For A: DiffBind MA plot
Popular Question 14 months ago, created a question with more than 1,000 views. For DiffBind Question
Popular Question 14 months ago, created a question with more than 1,000 views. For minOverlap in DiffBind in R- what does it mean?
Scholar 14 months ago, created an answer that has been accepted. For A: DiffBind Heatmap Omitting Results?
Scholar 14 months ago, created an answer that has been accepted. For A: Diffbind and dba.peakset vs dba.overlap
Scholar 14 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Guru 15 months ago, received more than 100 upvotes.
Popular Question 15 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 15 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 16 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 23 months ago, has more than 80 characters in the information field of the user's profile.

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